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Fungal elemental profiling unleashed through rapid laser-induced breakdown spectroscopy (LIBS). 通过快速激光诱导击穿光谱(LIBS)进行真菌元素分析。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-27 DOI: 10.1128/msystems.00919-24
Tomás A Rush, Ann M Wymore, Miguel Rodríguez, Sara Jawdy, Rytas J Vilgalys, Madhavi Z Martin, Hunter B Andrews

Elemental profiling of fungal species as a phenotyping tool is an understudied topic and is typically performed to examine plant tissue or non-biological materials. Traditional analytical techniques such as inductively coupled plasma-optical emission spectroscopy (ICP-OES) and inductively coupled plasma-mass spectrometry (ICP-MS) have been used to identify elemental profiles of fungi; however, these techniques can be cumbersome due to the difficulty of preparing samples. Additionally, the instruments used for these techniques can be expensive to procure and operate. Laser-induced breakdown spectroscopy (LIBS) is an alternative elemental analytical technique-one that is sensitive across the periodic table, easy to use on various sample types, and is cost-effective in both procurement and operation. LIBS has not been used on axenic filamentous fungal isolates grown in substrate media. In this work, as a proof of concept, we used LIBS on two genetically distinct fungal species grown on a nutrient-rich and nutrient-poor substrate media to determine whether robust elemental profiles can be detected and whether differences between the fungal isolates can be identified. Our results demonstrate a distinct correlation between fungal species and their elemental profile, regardless of the substrate media, as the same strains shared a similar uptake of carbon, zinc, phosphorus, manganese, and magnesium, which could play a vital role in their survival and propagation. Independently, each fungal species exhibited a unique elemental profile. This work demonstrates a unique and valuable approach to rapidly phenotype fungi through optical spectroscopy, and this approach can be critical in understanding these fungi's behavior and interactions with the environment.

Importance: Historically, ionomics, the elemental profiling of an organism or materials, has been used to understand the elemental composition in waste materials to identify and recycle heavy metals or rare earth elements, identify the soil composition in space exploration on the moon or Mars, or understand human disorders or disease. To our knowledge, ionomic profiling of microbes, particularly fungi, has not been investigated to answer applied and fundamental biological questions. The reason is that current ionomic analytical techniques can be laborious in sample preparation, fail to measure all potential elements accurately, are cost-prohibitive, or provide inconsistent results across replications. In our previous efforts, we explored whether laser-induced breakdown spectroscopy (LIBS) could be used in determining the elemental profiles of poplar tissue, which was successful. In this proof-of-concept endeavor, we undertook a transdisciplinary effort between applied and fundamental mycology and elemental analytical techniques to address the biological question of how LIBS can used for fungi grown axenically in a nutrient-rich and nutrient-poor environment.

作为一种表型工具,真菌物种的元素分析是一个研究不足的课题,通常是对植物组织或非生物材料进行检测。传统的分析技术,如电感耦合等离子体-光学发射光谱分析法(ICP-OES)和电感耦合等离子体-质谱分析法(ICP-MS),已被用于鉴定真菌的元素谱;然而,由于制备样品的困难,这些技术可能比较麻烦。此外,这些技术所使用的仪器采购和操作成本也很高。激光诱导击穿光谱(LIBS)是一种可供选择的元素分析技术--它对整个元素周期表都很敏感,易于在各种类型的样品上使用,而且在采购和操作方面都具有成本效益。LIBS 尚未用于在基质培养基中生长的轴丝真菌分离物。在这项工作中,作为概念验证,我们对生长在富营养和贫营养基质培养基上的两种基因不同的真菌物种使用了 LIBS,以确定是否能检测到稳健的元素谱,以及是否能识别真菌分离物之间的差异。我们的研究结果表明,无论基质介质如何,真菌种类与其元素特征之间都存在明显的相关性,因为相同的菌株对碳、锌、磷、锰和镁的吸收量相似,这可能对它们的生存和繁殖起着至关重要的作用。每种真菌都表现出独特的元素特征。这项工作展示了一种通过光学光谱快速对真菌进行表型的独特而有价值的方法,这种方法对于了解这些真菌的行为以及与环境的相互作用至关重要:从历史上看,离子组学,即对生物体或材料进行元素分析,一直被用于了解废料中的元素组成,以确定和回收重金属或稀土元素,确定月球或火星太空探索中的土壤成分,或了解人类失调或疾病。据我们所知,微生物(尤其是真菌)的离子组学分析还没有被研究用于回答应用和基础生物学问题。究其原因,目前的离子组分析技术在样品制备过程中可能很费力,无法准确测量所有潜在元素,成本高昂,或在不同重复中提供不一致的结果。在之前的工作中,我们探索了激光诱导击穿光谱(LIBS)是否可用于确定杨树组织的元素特征,并取得了成功。在这次概念验证工作中,我们在应用和基础真菌学以及元素分析技术之间进行了跨学科合作,以解决如何利用激光诱导击穿光谱(LIBS)测定在营养丰富和营养缺乏环境中轴向生长的真菌的生物学问题。
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引用次数: 0
Microbial genotoxin-elicited host DNA mutations related to mitochondrial dysfunction, a momentous contributor for colorectal carcinogenesis. 微生物基因毒性引发的宿主 DNA 变异与线粒体功能障碍有关,是导致结直肠癌发生的重要因素。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-27 DOI: 10.1128/msystems.00887-24
Xue Yang, Yumeng Gan, Yuting Zhang, Zhongjian Liu, Jiawei Geng, Wenxue Wang

Gut microbe dysbiosis increases repetitive inflammatory responses, leading to an increase in the incidence of colorectal cancer. Recent studies have revealed that specific microbial species directly instigate mutations in the host nucleus DNA, thereby accelerating the progression of colorectal cancer. Given the well-established role of mitochondrial dysfunction in promoting colorectal cancer, it is reasonable to postulate that gut microbes may induce mitochondrial gene mutations, thereby inducing mitochondrial dysfunction. In this review, we focus on gut microbial genotoxins and their known and potential targets in mitochondrial genes. Consequently, we propose that targeted disruption of genotoxin transport pathways may effectively reduce the rate of mitochondrial gene mutations and yield substantial benefits for the prevention of colorectal carcinogenesis.

肠道微生物菌群失调会增加重复性炎症反应,导致结直肠癌发病率上升。最近的研究发现,特定的微生物种类会直接导致宿主细胞核 DNA 发生突变,从而加速结直肠癌的发展。鉴于线粒体功能障碍在促进结直肠癌方面的作用已得到证实,我们有理由推测,肠道微生物可能会诱发线粒体基因突变,从而诱发线粒体功能障碍。在这篇综述中,我们将重点关注肠道微生物基因毒素及其线粒体基因的已知和潜在靶点。因此,我们建议,有针对性地破坏基因毒素转运途径可有效降低线粒体基因突变率,并为预防结直肠癌的发生带来巨大益处。
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引用次数: 0
Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes 基因组学和合成群落实验揭示酸包粉发酵剂微生物群中醋酸菌的关键代谢作用
IF 6.4 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 DOI: 10.1128/msystems.00537-24
H. B. RappaportNimshika P. J. SenewiratneSarah K. LucasBenjamin E. WolfeAngela M. Oliverio1Department of Biology, Syracuse University, Syracuse, New York, USA2Department of Biology, Tufts University, Medford, Massachusetts, USADaniel Garrido
mSystems, Ahead of Print.
mSystems, Ahead of Print.
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引用次数: 0
Demographic and zoological drivers of infectome diversity in companion cats with ascites. 患有腹水的伴侣猫感染组多样性的人口和动物学驱动因素。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-09 DOI: 10.1128/msystems.00636-24
Yankuo Sun, Jiabao Xing, Sijia Xu, Yue Li, Jianhao Zhong, Han Gao, Song Cheng, Jun Dong, Tianyou Zhang, Gang Lu, Guy Baele, Guihong Zhang

Cats (Felidae) have become an integral part of many households. However, our understanding of the full spectrum of pathogens affecting cats (referred to as the infectome) is limited, mainly due to the inadequacy of commonly used diagnostic tools in capturing the complete diversity of potential pathogens and the prevalence of pathogen co-infections. In this study, we employed a meta-transcriptomic approach to simultaneously characterize the infectome contributing to different disease syndromes and to investigate spatial, demographic, and ecological factors influencing pathogen diversity and community composition in a cohort of 27 hospitalized cats and seven stray cats. We identified 15 species of pathogens, with Candidatus Rickettsia tarasevichiae and Tritrichomonas foetus representing potential spillover risks. Importantly, although most cases of ascites hyperplasia were explained by coinfection with multiple pathogens, we identified the potential novel clinical outcomes of M. aubagnense infection among cats. We demonstrated that the increase in infectome diversity can be explained by a variety of predictors including age growth, temperature increase, and a higher proportion of females, with age growth presenting the strongest effect. Fine-scale analysis indicated that a higher diversity of infectomes were harbored in young cats rather than adult ones. Our results demonstrated that most feline diseases are better explained by the presence of virus-bacteria or virus-virus coinfection. This study serves as a timely endorsement for clinical diagnosis by vets to consider the cause of a disease based on a panel of cryptical co-infecting pathogens rather than on individual infectious agents.

Importance: Frequent studies reported the risks of cats as an intermediate host of zoonotic pathogens (e.g., SARS-CoV-2). Cats have a physically close interaction with their owners through activities like petting, kissing, and being licked on the cheek and hands. However, there are still limited studies that systematically investigate the infectome structure of cats. In this study, we employed a meta-transcriptomics approach to characterize 15 species of pathogens in cats, with Candidatus Rickettsia tarasevichiae first characterizing infection in diseased cats. Most feline diseases were better explained by the presence of virus-bacteria or virus-virus coinfection. The increase in infectome diversity could be influenced by a variety of predictors including age growth, temperature increase, and a higher proportion of females. A higher diversity of pathogens was harbored in young cats rather than adults. Importantly, we showed the value of linking the modern influx of meta-transcriptomics with comparative ecology and demography and of utilizing it to affirm that ecological and demographic variations impact the total infectome.

猫科动物已成为许多家庭不可或缺的一部分。然而,我们对影响猫的全部病原体(称为感染组)的了解还很有限,这主要是由于常用诊断工具不足以捕捉潜在病原体的全部多样性以及病原体合并感染的普遍性。在这项研究中,我们采用了元转录组学方法,同时描述了导致不同疾病综合征的感染组的特征,并调查了影响 27 只住院猫和 7 只流浪猫的病原体多样性和群落组成的空间、人口和生态因素。我们发现了 15 种病原体,其中塔拉塞维奇立克次体和胎生三联单胞菌具有潜在的外溢风险。重要的是,虽然大多数腹水增生病例都是由多种病原体共同感染引起的,但我们发现了猫感染 M. aubagnense 可能带来的新的临床结果。我们证明,感染组多样性的增加可以用多种预测因素来解释,包括年龄增长、温度升高和雌性比例增加,其中年龄增长的影响最大。精细分析表明,幼猫体内的感染组多样性高于成年猫。我们的研究结果表明,病毒-细菌或病毒-病毒共感染能更好地解释大多数猫科动物疾病。这项研究为兽医的临床诊断提供了及时的支持,即根据一组隐性合并感染病原体而不是单个感染病原体来考虑疾病的原因:重要性:经常有研究报告称,猫是人畜共患病原体(如 SARS-CoV-2)的中间宿主。猫通过抚摸、亲吻、舔舐脸颊和手等活动与主人进行亲密的身体接触。然而,系统研究猫感染组结构的研究仍然有限。在这项研究中,我们采用元转录组学方法描述了猫体内15种病原体的特征,其中塔拉塞维奇立克次体首先描述了病猫感染的特征。病毒-细菌或病毒-病毒共感染能更好地解释大多数猫科动物疾病。感染组多样性的增加可能受到多种因素的影响,包括年龄增长、温度升高和雌性比例增加。幼猫体内的病原体多样性高于成年猫。重要的是,我们展示了将现代大量涌入的元转录组学与比较生态学和人口统计学联系起来的价值,以及利用元转录组学确认生态学和人口统计学变化对总感染组产生影响的价值。
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引用次数: 0
Genomic analysis of antibiotic resistance genes and mobile genetic elements in eight strains of nontyphoid Salmonella. 八株非伤寒沙门氏菌耐抗生素基因和移动遗传因子的基因组分析。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-19 DOI: 10.1128/msystems.00586-24
Haibing Liu, Lijie Zheng, Huimin Fan, Ji Pang

Nontyphoidal Salmonella (NTS) is the main etiological agent of human nontyphoidal salmonellosis. The aim of this study was to analyze the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance (AMR) genes from eight strains of NTS detected in Zhenjiang City, Jiangsu Province, China. Fecal samples from outpatients with food-borne diarrhea were collected in 2022. The NTS isolates were identified, and their susceptibility was tested with the Vitek 2 Compact system. The genomes of the NTS isolates were sequenced with the Illumina NovaSeq platform and Oxford Nanopore Technologies platform. The AMR genes and mobile genetic elements (MGEs) were predicted with the relevant open access resources. Eight strains of NTS were isolated from 153 specimens, and Salmonella Typhimurium ST19 was the most prevalent serotype. The AMR gene with the highest detection rate was AAC(6')-Iaa (10.5%) followed by TEM-1 (7.9%), sul2 (6.6%), and tet(A) (5.3%). Eleven MGEs carrying 34 AMR genes were identified on the chromosomes of 3 of the 8 NTS, including 3 resistance islands, 6 composite transposons (Tns), and 2 integrons. Eighteen plasmids carrying 40 AMR genes were detected in the 8 NTS strains, including 6 mobilizable plasmids, 3 conjugative plasmids, and 9 nontransferable plasmids, 7 of which carried 10 composite Tns and 3 integrons. This study provided a theoretical basis, from a genetic perspective, for the prevention and control of NTS resistance in Zhenjiang City.

Importance: Human nontyphoidal salmonellosis is one of the common causes of bacterial food-borne illnesses, with significant social and economic impacts, especially those caused by invasive multidrug-resistant nontyphoidal Salmonella, which entails high morbidity and mortality. Antimicrobial resistance is mainly mediated by drug resistance genes, and mobile genetic elements play key roles in the capture, accumulation, and dissemination of antimicrobial resistance genes. Therefore, it is necessary to study the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance genes of nontyphoidal Salmonella to prevent the spread of multidrug-resistant nontyphoidal Salmonella.

非伤寒沙门氏菌(NTS)是人类非伤寒沙门氏菌病的主要病原菌。本研究旨在分析中国江苏省镇江市检出的8株NTS的流行病学特征和抗菌药耐药性(AMR)基因的水平转移机制。该研究收集了 2022 年食源性腹泻门诊患者的粪便样本。对 NTS 分离物进行了鉴定,并使用 Vitek 2 Compact 系统检测了它们的药敏性。用 Illumina NovaSeq 平台和 Oxford Nanopore Technologies 平台对 NTS 分离物的基因组进行了测序。利用相关开放资源对 AMR 基因和移动遗传元件(MGEs)进行了预测。从 153 份标本中分离出 8 株 NTS 菌株,伤寒沙门氏菌 ST19 是最常见的血清型。检出率最高的 AMR 基因是 AAC(6')-Iaa (10.5%),其次是 TEM-1 (7.9%)、sul2 (6.6%) 和 tet(A) (5.3%)。在 8 个 NTS 中的 3 个的染色体上发现了 11 个携带 34 个 AMR 基因的 MGE,包括 3 个抗性岛、6 个复合转座子(Tns)和 2 个整合子。在 8 株 NTS 中检测到携带 40 个 AMR 基因的 18 个质粒,包括 6 个可迁移质粒、3 个共轭质粒和 9 个不可迁移质粒,其中 7 个质粒携带 10 个复合转座子和 3 个整合子。该研究从遗传学角度为镇江市防控NTS耐药性提供了理论依据:人类非伤寒沙门氏菌病是细菌性食源性疾病的常见病因之一,具有重大的社会和经济影响,尤其是由具有多重耐药性的侵袭性非伤寒沙门氏菌引起的非伤寒沙门氏菌病,具有很高的发病率和死亡率。抗菌药耐药性主要是由耐药基因介导的,而移动遗传因子在抗菌药耐药基因的捕获、积累和传播中起着关键作用。因此,有必要研究非伤寒沙门氏菌抗菌基因的流行病学特征和水平转移机制,以防止耐多药非伤寒沙门氏菌的传播。
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引用次数: 0
Essential genes for Haemophilus parainfluenzae survival and biofilm growth. 副流感嗜血杆菌存活和生物膜生长的重要基因
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-21 DOI: 10.1128/msystems.00674-24
Thais H de Palma, Chris Powers, Morgan J McPartland, Jessica Mark Welch, Matthew Ramsey

Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.

副流感嗜血杆菌(Hp)是一种革兰氏阴性菌,在人类口腔中高度流行且数量众多,是一种不常见的口腔外机会性病原体。Hp 在口腔中占据多种生境,包括龈上菌斑生物膜。人们对 Hp 在健康的生物膜中如何与其周围环境相互作用以及它作为机会性病原体的致病机制知之甚少。为了解决这个问题,我们在体外有氧和无氧生物膜中鉴定了基本基因组和条件基本基因。通过对 ATCC33392 型菌株(Hp 392)和口腔分离株 EL1(Hp EL1)这两种菌株的高饱和度海洋转座子文库进行转座子插入测序(TnSeq),我们发现 Hp 392 和 Hp EL1 的基本基因组分别由 395 个(20%)和 384 个(19%)基因组成。核心基本基因组由 341 个(17%)基本基因组成,在两个菌株之间是一致的,由与遗传信息处理、碳水化合物、蛋白质和能量代谢相关的基因组成。我们还发现了有氧和厌氧生物膜生长的条件性必需基因,这些基因在两种菌株中都与碳水化合物和能量代谢有关。RNAseq 分析表明,厌氧生长过程中上调的大多数基因对 Hp 392 的厌氧生存并不重要。该文库的完成以及在这些条件下进行的分析使我们对副流感病毒在不同氧气条件下的基本生物学特性有了基本的了解,这与其在体内的生存环境相似。该文库为研究与人类口腔栖息地中许多微生物物种密切接触的生物体的条件性基本基因提供了一个宝贵的工具。副流感嗜血杆菌与良好的口腔健康息息相关,并可能在保持健康宿主状态方面发挥作用。此外,副流感病毒还可在口腔外引起机会性感染。尽管副流感嗜血杆菌是人类微生物组中如此常见和丰富的一部分,但迄今为止,人们对其如何在人类宿主中定植还知之甚少。在这里,我们展示了一种强大工具--TnSeq 文库--的创建和使用,该文库可用于鉴定该生物完全生长所必需的基因,以及在不同氧气状态下生长所必需的条件基因,而这正是该生物在人类宿主中可能遇到的情况。这一工具和这些数据为进一步研究这种可能在保护人类健康方面发挥作用的相对未知的生物体奠定了基础。
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引用次数: 0
Genetic requirements for uropathogenic E. coli proliferation in the bladder cell infection cycle 膀胱细胞感染周期中尿路致病性大肠杆菌增殖的遗传要求
IF 6.4 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 DOI: 10.1128/msystems.00387-24
Daniel G. MediatiTamika A. BlairAriana CostasLeigh G. MonahanBill SöderströmIan G. CharlesIain G. Duggin1Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia2Institut Cochin, INSERM U1016, Université de Paris, Paris, France3Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom4Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United KingdomJoshua E. Elias
mSystems, Ahead of Print.
mSystems, Ahead of Print.
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引用次数: 0
Whole-genome sequencing for antimicrobial surveillance: species-specific quality thresholds and data evaluation from the network of the European Union Reference Laboratory for Antimicrobial Resistance genomic proficiency tests of 2021 and 2022. 用于抗菌素监测的全基因组测序:2021 年和 2022 年欧盟抗菌素耐药性参考实验室基因组能力测试网络的特定物种质量阈值和数据评估。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-06 DOI: 10.1128/msystems.00160-24
Lauge Holm Sørensen, Susanne Karlsmose Pedersen, Jacob Dyring Jensen, Niamh Lacy-Roberts, Athina Andrea, Michael S M Brouwer, Kees T Veldman, Yan Lou, Maria Hoffmann, Rene S Hendriksen

As antimicrobial resistance (AMR) surveillance shifts to genomics, ensuring the quality of whole-genome sequencing (WGS) data produced across laboratories is critical. Participation in genomic proficiency tests (GPTs) not only increases individual laboratories' WGS capacity but also provides a unique opportunity to improve species-specific thresholds for WGS quality control (QC) by repeated resequencing of distinct isolates. Here, we present the results of the EU Reference Laboratory for Antimicrobial Resistance (EURL-AR) network GPTs of 2021 and 2022, which included 25 EU national reference laboratories (NLRs). A total of 392 genomes from 12 AMR-bacteria were evaluated based on WGS QC metrics. Two percent (n = 9) of the data were excluded, due to contamination, and 11% (n = 41) of the remaining genomes were identified as outliers in at least one QC metric and excluded from computation of the adjusted QC thresholds (AQT). Two QC metric correlation groups were identified through linear regression. Eight percent (n = 28) of the submitted genomes, from 11 laboratories, failed one or more of the AQTs. However, only three laboratories (12%) were identified as underperformers, failing across AQTs for uncorrelated QC metrics in at least two genomes. Finally, new species-specific thresholds for "N50" and "number of contigs > 200 bp" are presented for guidance in routine laboratory QC. The continued participation of NRLs in GPTs will reveal WGS workflow flaws and improve AMR surveillance data. GPT data will continue to contribute to the development of reliable species-specific thresholds for routine WGS QC, standardizing sequencing data QC and ensure inter- and intranational laboratory comparability.IMPORTANCEIllumina next-generation sequencing is an integral part of antimicrobial resistance (AMR) surveillance and the most widely used whole-genome sequencing (WGS) platform. The high-throughput, relative low-cost, high discriminatory power, and rapid turnaround time of WGS compared to classical biochemical methods means the technology will likely remain a fundamental tool in AMR surveillance and public health. In this study, we present the current level of WGS capacity among national reference laboratories in the EU Reference Laboratory for AMR network, summarizing applied methodology and statistically evaluating the quality of the obtained sequence data. These findings provide the basis for setting new and revised thresholds for quality metrics used in routine WGS, which have previously been arbitrarily defined. In addition, underperforming participants are identified and encouraged to evaluate their workflows to produce reliable results.

随着抗菌药耐药性 (AMR) 监控向基因组学转变,确保各实验室生成的全基因组测序 (WGS) 数据的质量至关重要。参加基因组能力测试(GPT)不仅能提高单个实验室的 WGS 能力,还能提供一个独特的机会,通过反复对不同的分离物进行重新测序来提高 WGS 质量控制(QC)的物种特异性阈值。在此,我们介绍了欧盟抗菌药物耐药性参考实验室(EURL-AR)网络 2021 年和 2022 年 GPT 的结果,其中包括 25 个欧盟国家参考实验室(NLR)。根据 WGS QC 指标对来自 12 种 AMR 细菌的共 392 个基因组进行了评估。由于污染,2%(n = 9)的数据被排除在外,其余基因组中的 11%(n = 41)在至少一个 QC 指标中被确定为异常值,并在计算调整后的 QC 阈值 (AQT) 时被排除在外。通过线性回归确定了两个 QC 指标相关组。11个实验室提交的基因组中有8%(n = 28)未能通过一个或多个AQT。不过,只有 3 个实验室(12%)被认定为表现不佳,至少有两个基因组的非相关 QC 指标在所有 AQTs 中均不合格。最后,提出了 "N50 "和 "等位基因数 > 200 bp "的新物种特定阈值,以指导实验室的常规质量控制。NRL 继续参与 GPT 将揭示 WGS 工作流程的缺陷并改进 AMR 监测数据。GPT 数据将继续促进为 WGS 常规质控制定可靠的物种特异性阈值,使测序数据质控标准化,并确保实验室间和实验室内的可比性。重要意义Illumina 下一代测序是抗菌素耐药性 (AMR) 监控不可或缺的一部分,也是应用最广泛的全基因组测序 (WGS) 平台。与传统的生化方法相比,WGS 具有高通量、相对低成本、高分辨力和快速周转时间等特点,这意味着该技术很可能继续成为 AMR 监测和公共卫生的基本工具。在本研究中,我们介绍了欧盟 AMR 参考实验室网络中各国参考实验室目前的 WGS 能力水平,总结了应用方法并对所获序列数据的质量进行了统计评估。这些发现为设定常规 WGS 质量指标的新阈值和修订阈值提供了依据,而这些阈值以前都是任意定义的。此外,还发现了表现不佳的参与者,并鼓励他们评估自己的工作流程,以产生可靠的结果。
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引用次数: 0
Ruminal microbial metagenomes and host transcriptomes shed light on individual variability in the growth rate of lambs before weaning: the regulated mechanism and potential long-term effect on the host. 反刍微生物元基因组和宿主转录组揭示了羔羊断奶前生长速度的个体差异:调节机制和对宿主的潜在长期影响。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-20 DOI: 10.1128/msystems.00873-24
Fan Hu, Yan Cheng, Bing Fan, Wei Li, Bingsen Ye, Zhiwu Wu, Zhiliang Tan, Zhixiong He

Weaning weight is a reflection of management during the breastfeeding phase and will influence animal performance in subsequent phases, considered important indicators within production systems. The aims of this study were as follows: (i) to investigate variability in the growth rate among individual lambs from ewes rearing single or twin lambs fed with two different diets and (ii) to explore the molecular mechanisms regulating the growth rate and the potential long-term effects on the host. No significant change in lamb average daily gain (ADG) was observed in litter size and diet treatment, and there were large variations among individual lambs (ranging from 0.13 to 0.41 kg/day). Further analysis was conducted on serum amino acids, rumen fermentation characteristics, rumen metagenomics and transcriptome, and hepatic transcriptome of lambs with extremely high (HA; n = 6) and low (LA; n = 6) ADG. We observed significant increases in serum lysine, leucine, alanine, and phenylalanine in the HA group. The metagenome revealed that the HA group presented a higher rumen propionate molar proportion via increasing gene abundance in the succinate pathway for propionate synthesis. For the rumen transcriptome, higher expressed gene sets in the HA group were mainly related to rumen epithelial growth, including cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, and adherens junction. For the liver transcriptome, the upregulated KEGG pathways in the HA group were primarily associated with fatty acid degradation, glyoxylate and dicarboxylate metabolism, cholesterol metabolism, and the immune system. This research suggests that preweaning lambs with high ADG may benefit from rumen development and enhanced liver metabolic and immune function.

Importance: There is accumulating evidence indicating that the early-life rumen microbiome plays vital roles in rumen development and microbial fermentation, which subsequently affects the growth of young ruminants. The liver is also vital to regulate the metabolism and distribution of nutrients. Our results demonstrate that lambs with high average daily gain (ADG) enhanced microbial volatile fatty acid (VFA) metabolism toward rumen propionate and serum amino acid (AA) production to support host growth. The study highlights that high ADG in the preweaning period is beneficial for the rumen development and liver energy metabolism, leading to better growth later in life. Overall, this study explores the molecular mechanisms regulating the growth rate and the potential long-term effects of increased growth rate on the host metabolism, providing fundamental knowledge about nutrient manipulation in pre-weaning.

断奶体重反映了哺乳阶段的管理情况,并将影响动物在随后阶段的表现,被视为生产系统中的重要指标。本研究的目的如下(i) 研究用两种不同日粮饲喂单羔或双羔的母羊所产羔羊个体生长率的变化;(ii) 探索调节生长率的分子机制以及对宿主的潜在长期影响。在窝产仔数和日粮处理中,未观察到羔羊平均日增重(ADG)有明显变化,而且羔羊个体之间的差异很大(从 0.13 到 0.41 千克/天不等)。我们对ADG极高(HA;n = 6)和极低(LA;n = 6)羔羊的血清氨基酸、瘤胃发酵特征、瘤胃元基因组学和转录组以及肝脏转录组进行了进一步分析。我们观察到,HA 组的血清赖氨酸、亮氨酸、丙氨酸和苯丙氨酸明显增加。元基因组显示,通过增加丙酸合成琥珀酸途径中的基因丰度,HA 组的瘤胃中丙酸的摩尔比例较高。在瘤胃转录组中,HA组表达较高的基因集主要与瘤胃上皮生长有关,包括细胞因子-细胞因子受体相互作用、Jak-STAT信号通路和粘连接头。在肝脏转录组中,HA 组中上调的 KEGG 通路主要与脂肪酸降解、乙醛酸和二羧酸代谢、胆固醇代谢以及免疫系统有关。这项研究表明,ADG 高的断奶前羔羊可能受益于瘤胃发育和肝脏代谢及免疫功能的增强:越来越多的证据表明,生命早期的瘤胃微生物群在瘤胃发育和微生物发酵中发挥着重要作用,进而影响幼年反刍动物的生长。肝脏对调节营养物质的代谢和分配也至关重要。我们的研究结果表明,平均日增重(ADG)高的羔羊会增强微生物挥发性脂肪酸(VFA)的代谢,促进瘤胃丙酸和血清氨基酸(AA)的产生,从而支持宿主的生长。该研究强调,断奶前的高日增重有利于瘤胃发育和肝脏能量代谢,从而使犊牛日后的生长更好。总之,本研究探讨了调节生长速度的分子机制以及生长速度提高对宿主代谢的潜在长期影响,为断奶前的营养调控提供了基础知识。
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引用次数: 0
Antibacterial effect of phage cocktails and phage-antibiotic synergy against pathogenic Klebsiella pneumoniae. 噬菌体鸡尾酒和噬菌体-抗生素协同作用对致病性肺炎克雷伯氏菌的抗菌效果。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-21 DOI: 10.1128/msystems.00607-24
Mengshi Zhao, Hongru Li, Dehao Gan, Mengzhu Wang, Hui Deng, Qiu E Yang

The global rise of antibiotic resistance has renewed interest in phage therapy, as an alternative to antibiotics to eliminate multidrug-resistant (MDR) bacterial pathogens. However, optimizing the broad-spectrum efficacy of phage therapy remains a challenge. In this study, we addressed this issue by employing strategies to improve antimicrobial efficacy of phage therapy against MDR Klebsiella pneumoniae strains, which are notorious for their resistance to conventional antibiotics. This includes the selection of broad host range phages, optimization of phage formulation, and combinations with last-resort antibiotics. Our findings unveil that having a broad host range was a dominant trait of isolated phages, and increasing phage numbers in combination with antibiotics significantly enhanced the suppression of bacterial growth. The decreased incidence of bacterial infection was explained by a reduction in pathogen density and emergence of bacterial resistance. Furthermore, phage-antibiotic synergy (PAS) demonstrated considerable broad-spectrum antibacterial potential against different clades of clinical MDR K. pneumoniae pathogens. The improved treatment outcomes of optimized PAS were also evident in a murine model, where mice receiving optimized PAS therapy demonstrated a reduced bacterial burden in mouse tissues. Taken together, these findings offer an important development in optimizing PAS therapy and its efficacy in the elimination of MDR K. pneumoniae pathogens.

Importance: The worldwide spread of antimicrobial resistance (AMR) has posed a great challenge to global public health. Phage therapy has become a promising alternative against difficult-to-treat pathogens. One important goal of this study was to optimize the therapeutic efficiency of phage-antibiotic combinations, known as phage-antibiotic synergy (PAS). Through comprehensive analysis of the phenotypic and genotypic characteristics of a large number of CRKp-specific phages, we developed a systematic model for phage cocktail combinations. Crucially, our finding demonstrated that PAS treatments not only enhance the bactericidal effects of colistin and tigecycline against multidrug-resistant (MDR) K. pneumoniae strains in in vitro and in vivo context but also provide a robust response when antibiotics fail. Overall, the optimized PAS therapy demonstrates considerable potential in combating diverse K. pneumoniae pathogens, highlighting its relevance as a strategy to mitigate antibiotic resistance threats effectively.

全球抗生素耐药性的上升再次激发了人们对噬菌体疗法的兴趣,它可以替代抗生素消灭耐多药(MDR)细菌病原体。然而,优化噬菌体疗法的广谱疗效仍是一项挑战。在这项研究中,我们针对这一问题采用了一些策略,以提高噬菌体疗法对耐多药肺炎克雷伯菌株的抗菌效力。这包括选择广泛宿主范围的噬菌体、优化噬菌体配方以及与最后的抗生素联合使用。我们的研究结果表明,宿主范围广是分离出的噬菌体的主要特征,增加噬菌体数量并与抗生素结合使用可显著增强对细菌生长的抑制作用。细菌感染率降低的原因是病原体密度降低和细菌抗药性的出现。此外,噬菌体-抗生素协同作用(PAS)对不同支系的临床 MDR 肺炎克氏病原体具有相当大的广谱抗菌潜力。在小鼠模型中,优化 PAS 的治疗效果也得到了明显改善,接受优化 PAS 治疗的小鼠在小鼠组织中的细菌负荷减少。综上所述,这些发现为优化 PAS 疗法及其消除 MDR 肺炎克氏病原体的疗效提供了重要进展:抗菌药耐药性(AMR)在全球的蔓延给全球公共卫生带来了巨大挑战。噬菌体疗法已成为对付难治病原体的一种有前途的替代疗法。本研究的一个重要目标是优化噬菌体-抗生素组合的治疗效率,即噬菌体-抗生素协同作用(PAS)。通过全面分析大量 CRKp 特异性噬菌体的表型和基因型特征,我们建立了噬菌体鸡尾酒组合的系统模型。重要的是,我们的研究结果表明,PAS疗法不仅能在体外和体内增强可乐定和替加环素对耐多药(MDR)肺炎克氏菌菌株的杀菌效果,还能在抗生素失效时提供强有力的反应。总之,优化后的 PAS疗法在抗击多种肺炎克氏菌病原体方面具有相当大的潜力,突出了其作为一种有效缓解抗生素耐药性威胁的策略的相关性。
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