strain typing

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  • 文章类型: Journal Article
    全基因组测序(WGS)数据已为淋球菌传播的调查建立。抗菌素耐药性预测,人口结构确定和人口动态。各种生物信息学工具,存储库,服务和平台已用于管理和分析淋病奈瑟菌WGS数据集。这篇综述概述了105项已发表研究(截至2021年4月30日)中使用的各种生物信息学方法和资源。淋病奈瑟菌WGS数据集分析中的挑战,以及未来的生物信息学要求,也讨论了。
    Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.
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  • 文章类型: Journal Article
    Direct detection methods for Treponema pallidum include dark-field microscopy (DFM), direct fluorescence antibody (DFA) testing, immunohistochemistry (IHC), and nucleic acid amplification tests (NAATs). Here, we reviewed the relevant syphilis diagnostic literature to address 2 main questions with respect to T. pallidum direct detection techniques: \"What are the performance characteristics for each direct detection test for T. pallidum and what are the optimal specimen types for each test?\" and \"What options are available for T. pallidum molecular epidemiology?\" To answer these questions, we searched 5 electronic databases (OVID Medline, OVID Embase, CINAHL, Cochrane Library, and Scopus) from 1964 to 2017 using relevant search terms and identified 1928 articles, of which 37 met our inclusion criteria. DFM and DFA sensitivities ranged from 73% to 100% in cases of primary syphilis; and while sensitivity using silver stain histopathology for T. pallidum was generally low (0%-41%), higher performance characteristics were observed for T. pallidum-specific IHC (49-92%). Different genes have been targeted by T. pallidum-specific NAATs, with the majority of studies indicating that sensitivity is primarily dependent on the type of collected biological sample, with highest sensitivity observed in primary lesion exudate (75-95%). Given the rising incidence of syphilis, the development of direct, Food and Drug Administration-cleared T. pallidum NAATs should be considered an immediate priority.
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  • 文章类型: Journal Article
    艰难梭菌分型对于调查特定机构的暴发以及国家监测都是无价的。尽管流行的ribotype027(RT027)已经获得了大量的资源和关注,在过去的十年中,核糖106(RT106)变得更加普遍。本系统综述的目的是全面总结遗传决定因素,抗菌敏感性,流行病学,和由RT106引起的感染的临床结果。1999年至2019年间发表的共68篇文章被确定为与本综述相关。尽管RT106最初于1999年在英国被发现,但现在在全球范围内发现,并于2016年成为美国最流行的菌株。目前的数据表明,RT106含有tcdA和tcdB基因,缺乏二元毒素基因,并且在tcdC基因中没有任何缺失,这将其与其他流行菌株区分开来,包括病毒型027和078.有趣的是,RT106比其他菌株产生更多的孢子,包括RT027。总的来说,RT106对红霉素有很强的耐药性,克林霉素,氟喹诺酮类药物,和第三代头孢菌素。然而,在大多数研究中,MIC90比甲硝唑和万古霉素的流行病学临界值低1-2倍稀释度,从体外角度来看,这两种治疗方案都是可以接受的。少数可获得的临床结果研究得出结论,RT106引起的疾病不如RT027严重,但是当感染RT106菌株时,患者更有可能经历多次CDI复发。值得未来研究的具体领域包括遗传因素提供的潜在生存优势,以及对与RT106相关的临床结果进行更有力的研究。
    Clostridioides difficile typing is invaluable for the investigation of both institution-specific outbreaks as well as national surveillance. While the epidemic ribotype 027 (RT027) has received a significant amount of resources and attention, ribotype 106 (RT106) has become more prevalent throughout the past decade. The purpose of this systematic review was to comprehensively summarize the genetic determinants, antimicrobial susceptibility, epidemiology, and clinical outcomes of infection caused by RT106. A total of 68 articles published between 1999 and 2019 were identified as relevant to this review. Although initially identified in the United Kingdom in 1999, RT106 is now found worldwide and became the most prevalent strain in the United States in 2016. Current data indicate that RT106 harbors the tcdA and tcdB genes, lacks binary toxin genes, and does not contain any deletions in the tcdC gene, which differentiates it from other epidemic strains, including ribotypes 027 and 078. Interestingly, RT106 produces more spores than other strains, including RT027. Overall, RT106 is highly resistant to erythromycin, clindamycin, fluoroquinolones, and third-generation cephalosporins. However, the MIC90 in most studies are one to two fold dilutions below the epidemiologic cut-off values of metronidazole and vancomycin, suggesting both are acceptable treatment options from an in vitro perspective. The few clinical outcomes studies available concluded that RT106 causes less severe disease than RT027, but patients were significantly more likely to experience multiple CDI relapses when infected with a RT106 strain. Specific areas warranting future study include potential survival advantages provided by genetic elements as well as a more robust investigation of clinical outcomes associated with RT106.
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