Applications of sequencing technology in clinical microbial infection

Infectious diseases are a type of disease caused by pathogenic microorganisms. Although the discovery of antibiotics changed the treatment of infectious diseases and reduced the mortality of bacterial infections, resistant bacterial strains have emerged. Anti‐infective therapy based on aetiological evidence is the gold standard for clinical treatment, but the time lag and low positive culture rate of traditional methods of pathogen diagnosis leads to relative difficulty in obtaining the evidence of pathogens. Compared with traditional methods of pathogenic diagnosis, next‐generation and third‐generation sequencing technologies have many advantages in the detection of pathogenic microorganisms. In this review, we mainly introduce recent progress in research on pathogenic diagnostic technology and the applications of sequencing technology in the diagnosis of pathogenic microorganisms. This review provides new insights into the application of sequencing technology in the clinical diagnosis of microorganisms.     

Human diseases as representation of interspecies competition

Different aspects of competition between human and pathogenic microorganisms as well as their role in evolution of the human as biological species and development of its polymorphism were reviewed. Biological consequences of interaction between human and pathogenic microorganisms and also main factors of genetic selection such as tuberculosis, malaria, etc. were characterized. Numerous forms of polymorphism, which determine level of susceptibility and features of clinical course of many infections in humans, were described. It has been concluded that selective pressure of microorganisms results from direct selection due to excessive mortality of infected persons before integration in human genome as well as that immunologic pressure of mass immunization results in changes of pathogenic microorganisms populations leading to emergence of their antigenically distinct variants. New knowledge about competition between human and pathogenic microorganisms requires development of fundamentally new approaches in fight with infectious diseases.     

九种蕨类植物多糖提取物抗动植物病原菌活性

从9种蕨类植物中提取多糖,以苯酚-硫酸比色法测定其含量,并采用纸片法进行抗动植物病原菌实验。结果表明,9种蕨类多糖含量差别较大,其多糖提取物表现出不同程度的抑制动植物病原菌活性。     

水产品病原菌及其检测与控制技术研究进展

病原微生物一直以来是影响水产品质量安全的重要因素, 本文阐述了当前水产品中存在的主要病原微生物及其污染现状, 介绍了病原微生物快速检测新技术的研究进展, 并就如何控制水产品中病原微生物的污染, 提出预防措施和建议。     

New principles and criteria in assessing pathogenic and opportunistic microorganisms

Using the ecological and natural-science approaches, the authors have come to the conclusion that microorganisms, pathogenic for humans (animals), are their parasites for whom the disease of their biological host is the necessary condition of their existence as a biological species. And accordingly, microorganisms, opportunistic in humans (animals) are their parasites and commensals, as well as saprophytes, for whom the disease of their host is not the necessary condition of their existence in nature. The biological host is a symbion necessary for the existence of pathogenic and most opportunistic microorganisms, but for a pathogenic microorganism the disease of the host is the result of symbiotic relationships, while for an opportunistic microorganism the disease of the host is the consequence of disturbances in symbiotic relationships. Such view of pathogenicity is important for creating a scientifically grounded theory of the liquidation of human infectious diseases.     

Analysis of potential contamination factors in musculoskeletal tissues

Tissue Banks have become the main source for bone grafts, due to preference for homologous tissues. Notwithstanding the use of aseptic techniques for procurement of tissues and judicious selection of donors, microorganisms are frequently found in procured bones. Purpose of this study is to evaluate the factors that increase safety of procurement and minimize discard of procured tissues. Microbiological contamination was analyzed in 1271 musculoskeletal tissues removed from 138 multi-organ donors over a period extending from 2006 to 2016. Effects of various risk factors related with contamination were estimated using a logistic regression model. Microbiological contamination rate in the tissues was 17.1%; low pathogenic microorganisms were cultivated in 12.9% of the tissues, while highly pathogenic ones were cultivated in 4.2% of the tissues. Evolution of one single team was monitored during that period, verifying a fall in the general contamination level from 22.5 to 9.2%. Absence of antibiotics increased low pathogenic contamination risk. Every additional day in intensive care unit (ICU) increased the risk of highly pathogenic contamination. Time elapsed between death and the beginning of removal procedures was found to be relevant for both low pathogenic and highly pathogenic microorganisms. Among the studied factors, the following contributed for a significant increase in contamination by microorganisms in removed tissues: lack of use of prophylactic antibiotic therapy in donors, quantity of removed tissues, length of admission in ICU and the time elapsed between aortic clamping and beginning of the removal procedure.     

补体系统基因单核苷酸多态性及其与疾病的关系

天然免疫系统在病原微生物入侵的初始阶段发挥着重要的防御作用,其中补体系统可快速识别、杀伤和清除病原微生物,对疾病的发生、发展和转归起着重要的作用。文章综述了补体系统各成份单核苷酸多态性与疾病的关联研究进展,在DNA水平上揭示了补体系统遗传多态性对疾病发生、发展和转归的影响,对疾病的预防和个体化治疗具有重要的意义。     

Genome sequence of the probiotic bacterium Sporolactobacillus vineae SL153T

The novel Sporolactobacillus vineae SL153(T) strain has excellent intestinal adherence and growth inhibitory effect on pathogenic microorganisms, including Vibrio genus microorganisms, and therefore can be effectively used for the prevention and treatment of disease caused by pathogenic microorganisms. Here, we first report the draft genome sequence of a novel species in the genus Sporolactobacillus.     

Seasonal variability in bacterial and fungal diversity and community composition of the near-surface atmosphere in coastal megacity

Bacteria and fungi are ubiquitous in the near-surface atmosphere where they may impact on the surrounding environment and human health, especially in coastal megacities. However, the diversity, composition, and seasonal variations of these airborne microbes remain limited. This study investigated the airborne microbes of the near-surface atmosphere in coastal megacity Qingdao over one year. It was found that the sample in summer displayed the highest bacterial and fungal diversity, while sample in winter exhibited the lowest bacterial and fungal diversity. Proteobacteria was the dominating bacteria, and Dothideomycetes was the most dominating fungi in the near-surface atmosphere, which took up 53–76 and 49–78% relative abundance, respectively. However, the bacterial diversity and community composition had significant seasonal variations. These data suggest that a complex set of environmental factors, including landscaping ratio, solar radiation temperature, and marine microorganisms, can affect the composition of airborne microbes in the near-surface atmosphere in coastal megacity. The analysis of the pathogenic microorganisms or opportunistic pathogenic microorganisms existed in the near-surface atmosphere revealed that the relative abundance of pathogenic microorganisms in autumn was the highest. The main pathogenic microorganisms or opportunistic pathogenic microorganisms were Acinetobacter baumannii (accounting for up to 9.93% relative abundance), Staphylococcus epidermidis (accounting for up to 11.26% relative abundance), Mycobacterium smegmatis (accounting for up to 3.68% relative abundance), Xanthomonas oryzae pv. oryzae (accounting for up to 5.36% relative abundance), which may be related to certain human or plant diseases in specific environments or at certain seasons. Therefore, the investigation of airborne microbial communities of near-surface atmosphere in coastal megacities is very important to both the understanding of airborne microbes and public health.     

Antimicrobial activity of the synthesized non-allergenic urushiol derivatives

Synthesized urushiol derivatives possessing different carbon atomic length in the alkyl side chain inhibited the growth of food spoilage and pathogenic microorganisms. Particularly, non-allergenic 3-pentylcatechol showed a broad antimicrobial spectrum on an agar plate. Most food spoilage and pathogenic microorganisms were sensitive to urushiol derivatives in the liquid culture. The morphologies of the microorganisms were changed after treatment of 3-pentylcatechol.     

Src和Abl酪氨酸蛋白激酶家族参与病原微生物感染的研究进展

Src和Abl家族激酶属于非受体型酪氨酸激酶(Nonreceptor tyrosine kinase,NRTK)家族重要成员,广泛存在于各种细胞中,参与细胞内信号传递并调节细胞生理过程,它们在维持细胞、组织和器官稳态功能中发挥着至关重要的作用。研究表明,Src和Abl家族激酶通过多种机制参与病原微生物的感染(如与病原微生物的脯氨酸基序-PXXP互作)。因此,从Src和Abl家族激酶角度出发探究病原微生物感染机制逐渐成为一个热点。本文就Src和Abl家族激酶的结构特点以及参与病原微生物感染的研究报道进行综述,以期为病原微生物感染的致病机制、防控和药物研发提供参考。     

城市绿地微生物及其对城市化的响应

城市绿地微生物的稳定性是城市绿地发挥其重要生态系统功能的重要因素。人类世时代的快速城市化会改变城市绿地土壤理化性质、输入新兴污染物、加剧微生物生态系统潜在风险、改变微生物群落多样性及生态系统功能多样性,深远地影响了城市绿地的生态系统服务功能。本文综述了城市绿地微生物的特征,以及城市化进程对城市绿地微生物组(包括土壤、植物叶际和空气)、抗生素抗性基因、病原微生物和稀有物种群落的影响。与自然微生物相比,城市绿地微生物普遍具有较高的异质性,受人类活动影响大。同时,抗生素抗性基因水平以及人类致病菌数量则显著增加,体现了城市化对城市绿地生态系统健康和功能的扰动。今后研究中应更加关注城市化对于城市绿地微生物的影响,为其对人群健康影响风险评价提供可靠理论支持。     

Protein Languages Differ Depending on Microorganism Lifestyle

Few quantitative measures of genome architecture or organization exist to support assumptions of differences between microorganisms that are broadly defined as being free-living or pathogenic. General principles about complete proteomes exist for codon usage, amino acid biases and essential or core genes. Genome-wide shifts in amino acid usage between free-living and pathogenic microorganisms result in fundamental differences in the complexity of their respective proteomes that are size and gene content independent. These differences are evident across broad phylogenetic groups–a result of environmental factors and population genetic forces rather than phylogenetic distance. A novel comparative analysis of amino acid usage–utilizing linguistic analyses of word frequency in language and text–identified a global pattern of higher peptide word repetition in 376 free-living versus 421 pathogen genomes across broad ranges of genome size, G+C content and phylogenetic ancestry. This imprint of repetitive word usage indicates free-living microorganisms have a bias for repetitive sequence usage compared to pathogens. These findings quantify fundamental differences in microbial genomes relative to life-history function.     

Defensive properties of pyrrolizidine alkaloids against microorganisms

The understanding of the selection factors that drive chemical diversification of secondary metabolites of constitutive defence systems in plants, such as pyrrolizidine alkaloids (PAs), is still incomplete. Historically, plants always have been confronted with microorganisms. Long before herbivores existed on this planet, plants had to cope with microbial pathogens. Therefore, plant pathogenic microorganisms may have played an important role in the early evolution of the secondary metabolite diversity. In this review, we discuss the impact that plant-produced PAs have on plant-associated microorganisms. The objective of the review is to present the current knowledge on PAs with respect to anti-microbial activities, adaptation and detoxification by microorganisms, pathogenic fungi, root protection and PA induction. Many in vitro experiments showed effects of PAs on microorganisms. These results point to the potential of microorganisms to be important for the evolution of PAs. However, only a few in vivo studies have been published and support the results of the in vitro studies. In conclusion, the topics pointed out in this review need further exploration by carrying out ecological experiments and field studies.     

Opportunistic microorganisms: the causative agents of food toxicoinfections and acute intestinal diseases

The analysis of sporadic morbidity due to acute intestinal infections and toxicoinfections caused by potentially pathogenic microorganisms is presented. The hypothesis stating that different pathogenic agents have different levels of pathogenic potential at a given stage of their evolution is proposed. Microorganisms with a low level of pathogenicity potential are characterized by the prevalence of the syndrome of toxicoinfection and by the rarity or absence of the syndrome of an acute intestinal disease. The prevalence of the latter is characteristic of potentially pathogenic microbes with a high level of pathogenicity potential making them similar to complete parasites.     

Cell sorting of formalin-treated pathogenic Mycobacterium paratuberculosis expressing GFP

GFP is widely used as a molecular tool for the study of microbial pathogens. However, the manipulation of these pathogenic microorganisms poses a health threat to the laboratory worker, requiring biosafety level II or III containment. Although the GFPfluorophore is tolerant toformalin, a thorough analysis of this treatment on fluorescent output in prokaryotic systems has not been described. In addition, the analysis of microorganisms expressing GFP often depends on specialized equipment, which may not be housed in biosafety level II or III laboratories. Therefore, we sought to develop a safe and effective method for manipulating the GFP-expressing pathogenic bacterium Mycobacterium avium subsp, paratuberculosis (M. paratuberculosis) utilizing a formalin treatment that would permit the analysis of GFP fluorescence without requiring stringent biosafety containment. We demonstrate that formalin-treated M. paratuberculosis expresses 50% less fluorescence than viable cells, but this reduction is still compatible with spectrofluorometry and cell sorting. Furthermore, plasmid DNA that expresses GFP can be recovered efficiently from nonviable, sorted fluorescent cells. This approach is flexible, provides an additional margin of safety for laboratory personnel, and can be easily applied to other pathogenic microorganisms expressing GFP.     

MBL调控MASP激活补体系统

甘露聚糖结合凝集素(MBL;或甘露聚糖结合蛋白,MBP)是由相同的多肽链组成的寡聚物,它通过结合细胞表面的碳水化合物能够有效地识别侵入体内的多种致病微生物,并激活补体来杀灭病原微生物。MBL能与血清中其相关蛋白酶(MASP)结合,MASP包含3个丝氨酸蛋白酶MASP-1、MASP-2、MASP-3和非酶蛋白MAp19。研究显示,MBL通过2种机理调控MASP-2的活性,在先天性免疫中具有重要的作用。本文简要综述MBL调控MASP激活补体的作用机理。     

Jasmonates - Signals in Plant-Microbe Interactions

Within their environment, plants interact with a wide range of microorganisms, some of which are pathogenic and cause disease, and others that are beneficial and stimulate plant growth or activate natural defenses. To recognize and respond to this variety of pathogenic and beneficial microorganisms, plants have developed sophisticated strategies to perceive microorganisms and translate that perception into an appropriate adaptive response. This plant innate immune response is surprisingly complex and highly flexible in its capacity to recognize and respond to different invaders. Jasmonic acid and derivatives, collectively called jasmonates (JAs), have emerged as important signals in the regulation of plant responses to pathogenic and beneficial microorganisms. The complex interplay of JAs with the alarm signals salicylic acid (SA) and ethylene (ET) provides plants with a regulatory potential that shapes the ultimate outcome of the plant-microbe interaction. In this review, we present an overview of the key role of JAs in basal and induced resistance to pathogens, their possible implication in the establishment and functioning of beneficial plant-microbe associations; and our current knowledge on how the JA signaling pathway cross-communicates with SA- and ET-dependent signaling pathways to fine-tune defense.     

高校实验室病原微生物管理现状调查及对策

【背景】近年来埃博拉病毒等病原微生物大范围传播引发了严重的公共安全问题,生物实验室安全管理受到各国政府的高度重视。【目的】了解国内高校病原微生物的管理状况,为实验室生物安全管理提供针对性举措。【方法】在查阅资料、与生物安全管理人员座谈的基础上设计调查问卷,对50所高校的341名师生进行调查并统计分析。【结果】国内高校实验室在病原微生物的安全教育、安全管理制度建设、实验室规范化建造、生物废弃物处置、实验室安全设施维护等方面存在明显不足。【结论】高校应严格落实安全管理责任制,采取措施消除各类安全隐患。     

The contribution of melanin to microbial pathogenesis

Melanins are enigmatic pigments that are produced by a wide variety of microorganisms including several species of pathogenic bacteria, fungi and helminths. The study of melanin is difficult because these pigments defy complete biochemical and structural analysis. Nevertheless, the availability of new reagents in the form of monoclonal antibodies and melanin-binding peptides, combined with the application of various physical techniques, has provided insights into the process of melanization. Melanization is important in microbial pathogenesis because it has been associated with virulence in many microorganisms. Melanin appears to contribute to virulence by reducing the susceptibility of melanized microbes to host defence mechanisms. However, the interaction of melanized microbes and the host is complex and includes immune responses to melanin-related antigens. Production of melanin has also been linked to protection against environmental insults. Interference with melanization is a potential strategy for antimicrobial drug and pesticide development. The process of melanization poses fascinating problems in cell biology and provides a type of pathogenic strategy that is common to highly diverse pathogens.