Infectious microbes & diseases最新文献_第3页

Minimum Core Genome Sequence Typing of Brucella From China 中国布鲁氏菌最小核心基因组序列分型

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-11-04 DOI: 10.1097/IM9.0000000000000109

N. Zhao, B. Cui

Abstract The Gram-negative bacterial genus Brucella includes six classic species based on host specificity, pathogenicity and phenotypic differences. Four more Brucella species were identified in 2007. Although many Brucella genomes have been sequenced, genome sequences and analysis of Brucella strains isolated in China are still scarce. An efficient genome-based Brucella typing method is also needed. In this study, we used the minimum core genome (MCG) typing method to identify and type Brucella strains. Twenty Brucella isolates from China were newly sequenced. The genome sequences of 55 representative Brucella strains were downloaded. Among the 75 genomes, 1089 genes and 52,030 single nucleotide polymorphisms (SNPs) shared by all isolates were considered as the MCG genes and MCG SNPs. Using these 52,030 MCG SNPs, Brucella was divided into six MCG groups. In addition, average nucleotide identity (ANI) values and the distributions of 184 virulence genes were all computed. The proportions of virulence genes were 90.96%, 93.56%, 95.89%, 86.04%, 85.78% and 91.87% for MCG groups 1 to 6, respectively. The intragroup ANI values were higher than the intergroup values, further confirming the validity of the MCG taxonomy classification. Brucella melitensis and Brucella abortus, the two main Brucella species pathogenic to humans, were well separated from other species. With the development and cost reduction of next-generation sequencing, the MCG typing method can be used for rapid identification of Brucella, which can contribute to the rapid diagnosis of brucellosis and ensure timely and effective treatment.

根据宿主特异性、致病性和表型差异，革兰氏阴性细菌布鲁氏菌属包括6个经典种。2007年又发现了四种布鲁氏菌。虽然已经对许多布鲁氏菌基因组进行了测序，但中国分离的布鲁氏菌菌株的基因组序列和分析仍然很少。还需要一种高效的基于基因组的布鲁氏菌分型方法。本研究采用最小核心基因组(MCG)分型方法对布鲁氏菌菌株进行鉴定和分型。从中国分离的20株布鲁氏菌进行了新测序。下载55株代表性布鲁氏菌的基因组序列。在75个基因组中，共有1089个基因和52030个单核苷酸多态性(snp)被认为是MCG基因和MCG snp。利用这52,030个MCG snp，布鲁氏菌被分为6个MCG组。计算了184个毒力基因的平均核苷酸同一性(ANI)值和分布。MCG 1 ~ 6组毒力基因比例分别为90.96%、93.56%、95.89%、86.04%、85.78%和91.87%。组内ANI值高于组间ANI值，进一步证实了MCG分类分类的有效性。对人类致病的两种主要布鲁氏菌——melitensis布鲁氏菌和abortus布鲁氏菌与其他种类的布鲁氏菌分离较好。随着下一代测序技术的发展和成本的降低，MCG分型方法可用于布鲁氏菌的快速鉴定，有助于布鲁氏菌病的快速诊断和及时有效的治疗。

{"title":"Minimum Core Genome Sequence Typing of Brucella From China","authors":"N. Zhao, B. Cui","doi":"10.1097/IM9.0000000000000109","DOIUrl":"https://doi.org/10.1097/IM9.0000000000000109","url":null,"abstract":"Abstract The Gram-negative bacterial genus Brucella includes six classic species based on host specificity, pathogenicity and phenotypic differences. Four more Brucella species were identified in 2007. Although many Brucella genomes have been sequenced, genome sequences and analysis of Brucella strains isolated in China are still scarce. An efficient genome-based Brucella typing method is also needed. In this study, we used the minimum core genome (MCG) typing method to identify and type Brucella strains. Twenty Brucella isolates from China were newly sequenced. The genome sequences of 55 representative Brucella strains were downloaded. Among the 75 genomes, 1089 genes and 52,030 single nucleotide polymorphisms (SNPs) shared by all isolates were considered as the MCG genes and MCG SNPs. Using these 52,030 MCG SNPs, Brucella was divided into six MCG groups. In addition, average nucleotide identity (ANI) values and the distributions of 184 virulence genes were all computed. The proportions of virulence genes were 90.96%, 93.56%, 95.89%, 86.04%, 85.78% and 91.87% for MCG groups 1 to 6, respectively. The intragroup ANI values were higher than the intergroup values, further confirming the validity of the MCG taxonomy classification. Brucella melitensis and Brucella abortus, the two main Brucella species pathogenic to humans, were well separated from other species. With the development and cost reduction of next-generation sequencing, the MCG typing method can be used for rapid identification of Brucella, which can contribute to the rapid diagnosis of brucellosis and ensure timely and effective treatment.","PeriodicalId":73374,"journal":{"name":"Infectious microbes & diseases","volume":"5 1","pages":"29 - 35"},"PeriodicalIF":0.0,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42120037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Systematic Review on Antituberculosis Drug Discovery and Antimycobacterial Potential of Biologically Synthesized Silver Nanoparticles: Overview and Future Perspectives 抗结核药物发现和生物合成银纳米粒子抗分枝杆菌潜力的系统综述：综述和未来展望

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-11-01 DOI: 10.1097/IM9.0000000000000107

Christian K. Ezeh, C. Eze, U. Dibua, S. Emencheta

Abstract Rapid emergence and quick evolution of drug-resistant and aggressive mycobacterial strains have resulted in the present antimycobacterial drug crisis and the persistence of tuberculosis as a major public health problem. Green/biological nanotechnologies constitute an interesting area of research for discovering antimycobacterial agents. This review focused on the biological (green) synthesis of silver nanoparticles (AgNPs) as an alternative source of antimycobacterial agents. Data for this study were searched and screened from three electronic databases (Google Scholar, PubMed and ScienceDirect) following the Preferred Reporting Items for Systematic Reviews and Meta-analyses flowchart. Data from in total 17 eligible studies were reported in this systematic review. Twelve of the 17 studies used plants to fabricate AgNPs, whereas the remaining five studies used microorganisms (bacteria and/or fungi). Silver as part of silver nitrate (AgNO3) was the metal precursor reported for the synthesis of AgNPs in these studies. Silver nanoparticles were mostly spherical, with sizes ranging from 12 to 140 nm. Results based on minimum inhibitory concentrations varied between studies and were divided into three groups: (i) those more effective than the antibiotic (controls), (ii) those more effective than plant extracts, and (iii) those less effective than the antibiotic controls. In addition, little or no cytotoxicity effects were reported. Silver nanoparticles were also shown to be highly specific or selective toward mycobacterial strains. This systematic review highlights the antimycobacterial potential of biologically synthesized AgNPs, underscoring the possibility of discovering/developing new antimycobacterial agents using biological synthesis approaches with less toxicity and high selectivity.

摘要耐药和侵袭性分枝杆菌菌株的快速出现和快速进化导致了目前的抗分枝杆菌药物危机，并使结核病成为一个主要的公共卫生问题。绿色/生物纳米技术是发现抗分枝杆菌制剂的一个有趣的研究领域。这篇综述的重点是生物（绿色）合成银纳米颗粒（AgNPs）作为抗分枝杆菌剂的替代来源。根据系统评价首选报告项目和荟萃分析流程图，从三个电子数据库（Google Scholar、PubMed和ScienceDirect）中搜索和筛选本研究的数据。本系统综述共报告了17项符合条件的研究的数据。17项研究中有12项使用植物制造AgNP，而其余5项研究使用微生物（细菌和/或真菌）。银作为硝酸银（AgNO3）的一部分是这些研究中报道的用于合成AgNPs的金属前体。银纳米颗粒大多是球形的，尺寸在12至140nm之间。基于最小抑制浓度的结果在不同的研究中各不相同，并分为三组：（i）比抗生素更有效的（对照组），（ii）比植物提取物更有效的，以及（iii）比抗生素对照组更无效的。此外，很少或没有细胞毒性作用的报道。银纳米颗粒也被证明对分枝杆菌菌株具有高度特异性或选择性。这篇系统综述强调了生物合成的AgNPs的抗分枝杆菌潜力，强调了使用毒性小、选择性高的生物合成方法发现/开发新的抗分枝菌剂的可能性。

{"title":"A Systematic Review on Antituberculosis Drug Discovery and Antimycobacterial Potential of Biologically Synthesized Silver Nanoparticles: Overview and Future Perspectives","authors":"Christian K. Ezeh, C. Eze, U. Dibua, S. Emencheta","doi":"10.1097/IM9.0000000000000107","DOIUrl":"https://doi.org/10.1097/IM9.0000000000000107","url":null,"abstract":"Abstract Rapid emergence and quick evolution of drug-resistant and aggressive mycobacterial strains have resulted in the present antimycobacterial drug crisis and the persistence of tuberculosis as a major public health problem. Green/biological nanotechnologies constitute an interesting area of research for discovering antimycobacterial agents. This review focused on the biological (green) synthesis of silver nanoparticles (AgNPs) as an alternative source of antimycobacterial agents. Data for this study were searched and screened from three electronic databases (Google Scholar, PubMed and ScienceDirect) following the Preferred Reporting Items for Systematic Reviews and Meta-analyses flowchart. Data from in total 17 eligible studies were reported in this systematic review. Twelve of the 17 studies used plants to fabricate AgNPs, whereas the remaining five studies used microorganisms (bacteria and/or fungi). Silver as part of silver nitrate (AgNO3) was the metal precursor reported for the synthesis of AgNPs in these studies. Silver nanoparticles were mostly spherical, with sizes ranging from 12 to 140 nm. Results based on minimum inhibitory concentrations varied between studies and were divided into three groups: (i) those more effective than the antibiotic (controls), (ii) those more effective than plant extracts, and (iii) those less effective than the antibiotic controls. In addition, little or no cytotoxicity effects were reported. Silver nanoparticles were also shown to be highly specific or selective toward mycobacterial strains. This systematic review highlights the antimycobacterial potential of biologically synthesized AgNPs, underscoring the possibility of discovering/developing new antimycobacterial agents using biological synthesis approaches with less toxicity and high selectivity.","PeriodicalId":73374,"journal":{"name":"Infectious microbes & diseases","volume":"4 1","pages":"139 - 148"},"PeriodicalIF":0.0,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48629532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cytokine Profiling in Influenza A Virus and Staphylococcal (Co-)Infections 甲型流感病毒和葡萄球菌(Co-)感染的细胞因子谱分析

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-11-01 DOI: 10.1097/IM9.0000000000000108

Lea A. Tölken, Antje D. Paulikat, Fabian Cuypers, Sebastian B. Skorka, S. Hammerschmidt, N. Siemens

Abstract Influenza A virus and Staphylococcus aureus are common causative agents of pneumonia. Co-infections with these two pathogens frequently occur and are characterized, among others, by higher morbidity and mortality due to hyper-inflammation of the lungs. Here, we aimed to profile systemic and local cytokine composition at early acute stages of pneumonia in a murine model. All mice recovered from single influenza A virus and/or staphylococcal infections. In contrast, co-infections led to a severe clinical outcome. While distinct cytokine patterns were detected in lungs of single-pathogen-infected animals, co-infections combined both virus- and bacteria-driven responses. However, analyses of infected human primary monocytic cells as well as bronchial epithelial cells did not reflect murine profiles. Based on infectious dose, mainly bacteria-driven responses were noted. The impact of single cells to cytokine composition of the lungs and translation of murine studies to humans remains uncertain and warrants further studies.

甲型流感病毒和金黄色葡萄球菌是常见的肺炎病原体。这两种病原体的合并感染经常发生，其特点之一是由于肺部的高度炎症导致较高的发病率和死亡率。在这里，我们的目的是在小鼠模型中分析肺炎早期急性阶段的全身和局部细胞因子组成。所有小鼠均从单一甲型流感病毒和/或葡萄球菌感染中恢复。相反，合并感染导致严重的临床结果。虽然在单一病原体感染动物的肺部检测到不同的细胞因子模式，但合并感染结合了病毒和细菌驱动的反应。然而，对感染的人原代单核细胞和支气管上皮细胞的分析并没有反映小鼠的特征。根据感染剂量，主要注意到细菌驱动的反应。单细胞对肺部细胞因子组成的影响以及小鼠研究对人类的转化仍然不确定，需要进一步研究。

引用次数: 1

Identification of Persister Drug Combination Clinafloxacin + Cefuroxime + Gentamicin That Eradicates Persistent Pseudomonas aeruginosa Infection in a Murine Cystic Fibrosis Model 克林沙星+头孢呋辛+庆大霉素联合用药根除小鼠囊性纤维化模型中铜绿假单胞菌持续性感染的鉴定

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-10-27 DOI: 10.1097/IM9.0000000000000106

Yuting Yuan, R. Yee, N. Gour, Xinzhong Dong, Jie Feng, W. Shi, Y. Zhang

Abstract Pseudomonas aeruginosa can cause persistent infections, such as biofilm infections, in cystic fibrosis patients, which are difficult to cure due to non-growing persister bacteria that are not effectively killed by the current treatments. While antibiotic activity against growing P. aeruginosa is well documented, their activity against non-growing stationary phase cultures is less clear. Here, we evaluated six major classes of antibiotics, including cell wall and cell membrane inhibitors, protein synthesis inhibitors, DNA synthesis inhibitors, RNA synthesis inhibitors, sulfa drugs and nitrofurantoin, for their activity against growing and non-growing P. aeruginosa. We found that cell wall and cell membrane inhibitors (cefuroxime and colistin), DNA synthesis inhibitors (clinafloxacin) and sulfa drugs (sulfamethoxazole) had good activity against stationary-phase bacteria, while protein synthesis inhibitors (gentamicin), RNA synthesis inhibitor (rifampin) and nitrofurantoin showed relatively poor activity. Clinafloxacin was the only drug able to completely eradicate stationary-phase bacteria within four days. The cefuroxime + gentamicin + clinafloxacin combination was able to kill all bacteria from a biofilm within two days, whereas the clinically used drug combination cefuroxime + gentamicin/colistin only partially killed the biofilm bacteria. In a murine persistent cystic fibrosis lung infection model, only the cefuroxime + gentamicin + clinafloxacin drug combination eradicated all bacteria from the lungs, whereas clinafloxacin alone, cefuroxime + clinafloxacin or the currently recommended drug combination cefuroxime + gentamicin failed to do so. The complete eradication is a property of the clinafloxacin combination, as the otherwise identical levofloxacin combination did not clear the bacterial loads from the lungs. Our findings offer new therapeutic options for more effective treatment of persistent P. aeruginosa infections, with possible implications for treating other persistent infections.

摘要铜绿假单胞菌可导致囊性纤维化患者的持续感染，如生物膜感染，由于目前的治疗方法无法有效杀死不生长的持续细菌，这种感染很难治愈。虽然抗生素对生长中的铜绿假单胞菌的活性已被充分证明，但它们对非生长固定相培养物的活性尚不清楚。在这里，我们评估了六类主要的抗生素，包括细胞壁和细胞膜抑制剂、蛋白质合成抑制剂、DNA合成抑制剂、RNA合成抑制剂、磺胺类药物和呋喃妥因，它们对生长和非生长的铜绿假单胞菌的活性。我们发现细胞壁和细胞膜抑制剂（头孢呋辛和粘菌素）、DNA合成抑制剂（克林霉素）和磺胺类药物（磺胺甲恶唑）对固定相细菌具有良好的活性，而蛋白质合成抑制剂（庆大霉素）、RNA合成抑制剂（利福平）和呋喃妥因的活性相对较差。Clinafloxacin是唯一一种能够在四天内完全根除固定相细菌的药物。头孢呋辛+庆大霉素+克林霉素组合能够在两天内杀死生物膜中的所有细菌，而临床使用的药物组合头孢呋辛+庆大霉素/粘菌素仅部分杀死生物膜细菌。在小鼠持续性囊性纤维化肺部感染模型中，只有头孢呋辛+庆大霉素+克林沙星药物组合根除了肺部的所有细菌，而单独的克林沙星、头孢呋辛和克林沙星或目前推荐的药物组合头孢呋辛加庆大霉素未能做到这一点。完全根除是克林沙星组合的一个特性，因为在其他方面相同的左氧氟沙星组合不能清除肺部的细菌载量。我们的发现为更有效地治疗持续性铜绿假单胞菌感染提供了新的治疗选择，并可能对治疗其他持续性感染产生影响。

{"title":"Identification of Persister Drug Combination Clinafloxacin + Cefuroxime + Gentamicin That Eradicates Persistent Pseudomonas aeruginosa Infection in a Murine Cystic Fibrosis Model","authors":"Yuting Yuan, R. Yee, N. Gour, Xinzhong Dong, Jie Feng, W. Shi, Y. Zhang","doi":"10.1097/IM9.0000000000000106","DOIUrl":"https://doi.org/10.1097/IM9.0000000000000106","url":null,"abstract":"Abstract Pseudomonas aeruginosa can cause persistent infections, such as biofilm infections, in cystic fibrosis patients, which are difficult to cure due to non-growing persister bacteria that are not effectively killed by the current treatments. While antibiotic activity against growing P. aeruginosa is well documented, their activity against non-growing stationary phase cultures is less clear. Here, we evaluated six major classes of antibiotics, including cell wall and cell membrane inhibitors, protein synthesis inhibitors, DNA synthesis inhibitors, RNA synthesis inhibitors, sulfa drugs and nitrofurantoin, for their activity against growing and non-growing P. aeruginosa. We found that cell wall and cell membrane inhibitors (cefuroxime and colistin), DNA synthesis inhibitors (clinafloxacin) and sulfa drugs (sulfamethoxazole) had good activity against stationary-phase bacteria, while protein synthesis inhibitors (gentamicin), RNA synthesis inhibitor (rifampin) and nitrofurantoin showed relatively poor activity. Clinafloxacin was the only drug able to completely eradicate stationary-phase bacteria within four days. The cefuroxime + gentamicin + clinafloxacin combination was able to kill all bacteria from a biofilm within two days, whereas the clinically used drug combination cefuroxime + gentamicin/colistin only partially killed the biofilm bacteria. In a murine persistent cystic fibrosis lung infection model, only the cefuroxime + gentamicin + clinafloxacin drug combination eradicated all bacteria from the lungs, whereas clinafloxacin alone, cefuroxime + clinafloxacin or the currently recommended drug combination cefuroxime + gentamicin failed to do so. The complete eradication is a property of the clinafloxacin combination, as the otherwise identical levofloxacin combination did not clear the bacterial loads from the lungs. Our findings offer new therapeutic options for more effective treatment of persistent P. aeruginosa infections, with possible implications for treating other persistent infections.","PeriodicalId":73374,"journal":{"name":"Infectious microbes & diseases","volume":"5 1","pages":"21 - 28"},"PeriodicalIF":0.0,"publicationDate":"2022-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47845554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Vibrio Septicemia Diagnosed With Next-Generation Sequencing: A Case Report 用新一代测序诊断败血症弧菌:一例报告

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-10-02 DOI: 10.1097/IM9.0000000000000104

Zutao Chen, Xiao Liu, Yajuan Wang, Yun-hai Yao

Abstract Vibrio vulnificus and Vibrio parahaemolyticus are marine gram-negative bacilli that can cause septicemia and gastrointestinal and wound infections. Early suspicion, diagnosis and appropriate antibiotic therapy for those infections are essential as delay can adversely affect the outcome. Here, we report a patient who developed a V. vulnificus and V. parahaemolyticus infection after contact with a fishing net. The cause of infection was finally diagnosed by metagenomic next-generation sequencing. The patient required an emergency amputation of the upper- and middle-third of the right upper limb.

摘要创伤弧菌和副溶血性弧菌是海洋革兰氏阴性杆菌，可引起败血症、胃肠道和伤口感染。对这些感染进行早期怀疑、诊断和适当的抗生素治疗至关重要，因为延迟可能会对结果产生不利影响。在这里，我们报告了一名患者，他在接触渔网后感染了创伤弧菌和副溶血弧菌。感染原因最终通过宏基因组下一代测序得到诊断。患者需要紧急截肢右上肢的中三分之一和上三分之一。

引用次数: 0

The Utility of Voided Urine Samples as a Proxy for the Vaginal Microbiome and for the Prediction of Bacterial Vaginosis 排尿样本作为阴道微生物组和细菌性阴道病预测指标的应用

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-09-27 DOI: 10.1097/IM9.0000000000000103

Bin Zhu, Christopher Diachok, Laahirie Edupuganti, David J. Edwards, Jeffrey R. Donowitz, K. Tossas, A. Matveyev, Katherine M. Spaine, Vladimir Lee, M. Serrano, Gregory A. Buck

Abstract Recent work has shown that the vaginal microbiome exerts a strong impact on women's gynecological health. However, collection of vaginal specimens is invasive and requires previous clinical training or the involvement of a trained clinician. In contrast, urine sample collection is routine and noninvasive and does not require involvement of a clinician. We sought to compare the vaginal and urogenital microbiomes to assess the utility of voided urine samples as a proxy for the vaginal microbiome. Paired urogenital and vaginal samples were collected from pregnant women and characterized by 16S rRNA taxonomic profiling. We examined diversities and compositions of paired urogenital and vaginal microbiomes using five discrete strategies to explore the similarity between the vaginal and urogenital microbiomes. A strategy comparing the paired urogenital and vaginal microbiomes in which taxa were assigned using the STIRRUPS database and urine-specific taxa were removed showed no significant difference in diversity and composition between the paired urogenital and vaginal microbiomes. Moreover, the relative abundances of common vaginal taxa were linearly correlated with those in the paired urogenital microbiomes. These similarities suggest that voided urine samples could represent a noninvasive protocol for accurate profiling of the vaginal microbiome with likely clinical applications. Finally, a machine learning model was established in which the voided urine microbiome was compared favorably to the vaginal microbiome in predicting bacterial vaginosis.

摘要最近的研究表明，阴道微生物组对女性的妇科健康有很大影响。然而，阴道标本的采集是侵入性的，需要之前的临床培训或训练有素的临床医生的参与。相反，尿液样本采集是常规的和非侵入性的，不需要临床医生的参与。我们试图比较阴道和泌尿生殖道微生物组，以评估排泄尿液样本作为阴道微生物组替代品的效用。从孕妇身上采集成对的泌尿生殖道和阴道样本，并通过16S rRNA分类图谱进行表征。我们使用五种离散策略检测了配对的泌尿生殖道和阴道微生物组的多样性和组成，以探索阴道和泌尿生殖道微生物组之间的相似性。一项比较配对的泌尿生殖道和阴道微生物群的策略显示，配对的泌尿生殖器和阴道微生物组之间的多样性和组成没有显著差异，其中使用STIRRUPS数据库分配了分类群，并删除了尿液特异性分类群。此外，常见阴道分类群的相对丰度与配对的泌尿生殖微生物群中的相对丰度呈线性相关。这些相似之处表明，排泄的尿液样本可能是一种无创的方案，可以准确分析阴道微生物组，并可能在临床上应用。最后，建立了一个机器学习模型，在该模型中，在预测细菌性阴道病时，将排泄尿液微生物组与阴道微生物组进行了有利的比较。

{"title":"The Utility of Voided Urine Samples as a Proxy for the Vaginal Microbiome and for the Prediction of Bacterial Vaginosis","authors":"Bin Zhu, Christopher Diachok, Laahirie Edupuganti, David J. Edwards, Jeffrey R. Donowitz, K. Tossas, A. Matveyev, Katherine M. Spaine, Vladimir Lee, M. Serrano, Gregory A. Buck","doi":"10.1097/IM9.0000000000000103","DOIUrl":"https://doi.org/10.1097/IM9.0000000000000103","url":null,"abstract":"Abstract Recent work has shown that the vaginal microbiome exerts a strong impact on women's gynecological health. However, collection of vaginal specimens is invasive and requires previous clinical training or the involvement of a trained clinician. In contrast, urine sample collection is routine and noninvasive and does not require involvement of a clinician. We sought to compare the vaginal and urogenital microbiomes to assess the utility of voided urine samples as a proxy for the vaginal microbiome. Paired urogenital and vaginal samples were collected from pregnant women and characterized by 16S rRNA taxonomic profiling. We examined diversities and compositions of paired urogenital and vaginal microbiomes using five discrete strategies to explore the similarity between the vaginal and urogenital microbiomes. A strategy comparing the paired urogenital and vaginal microbiomes in which taxa were assigned using the STIRRUPS database and urine-specific taxa were removed showed no significant difference in diversity and composition between the paired urogenital and vaginal microbiomes. Moreover, the relative abundances of common vaginal taxa were linearly correlated with those in the paired urogenital microbiomes. These similarities suggest that voided urine samples could represent a noninvasive protocol for accurate profiling of the vaginal microbiome with likely clinical applications. Finally, a machine learning model was established in which the voided urine microbiome was compared favorably to the vaginal microbiome in predicting bacterial vaginosis.","PeriodicalId":73374,"journal":{"name":"Infectious microbes & diseases","volume":"4 1","pages":"149 - 156"},"PeriodicalIF":0.0,"publicationDate":"2022-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42007506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Global Transmission of Human Immunodeficiency Virus 1 Subtype C and Its Impact on the Circulation of B/C Recombination Strains in China 人免疫缺陷病毒1型C亚型的全球传播及其对中国B/C重组毒株传播的影响

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-09-15 DOI: 10.1097/IM9.0000000000000102

Zhanmou Liu, Yanling Liang, Yi Feng, Kang Li, Y. Shao

Abstract This study aimed to reconstruct the origin and worldwide epidemic history of human immunodeficiency virus (HIV) 1 subtype C and comprehend how HIV-1 subtype C was introduced into and spread throughout China in the form of B/C recombinant strains. Envelope sequences of HIV-1 subtype C and some other subtypes deposited before December 31, 2020 were downloaded from the Los Alamos HIV Database and the Chinese National Center for AIDS/STD Control and Prevention Database. The available sequences were screened for quality, and Bayesian analysis was used to build the maximum clade credibility evolutionary tree to analyze and judge the origin and spread of HIV-1 subtype C. HIV-1 subtype C originated in central Africa around 1952, then spread to southern Africa around 1969 and to eastern Africa around 1973. HIV-1 subtype C from southern Africa was introduced into India in 1977. HIV-1 subtype C of eastern Africa was introduced into Brazil in 1987. Indian HIV-1 subtype C was exported to China in three migration events during the period from 1986 to 1989. The two predominant recombinants in China (CRF07_BC and CRF08_BC) emerged in 1988 and 1990, respectively. Other B/C recombinants, namely, CRF64_BC, CRF61_BC and CRF62_BC, originated in 1993, 2002 and 2000, respectively. Our study has reconstructed the global origin and evolutionary history of HIV-1 subtype C. In addition, our study demonstrated that the Chinese HIV-1 subtype C originated from three related Indian lineages around the mid to late 1980s and, since then, has formed some B/C recombinants with subtype B that caused a widespread epidemic in China.

摘要本研究旨在重建人类免疫缺陷病毒（HIV）1亚型C的起源和全球流行史，了解HIV-1亚型C是如何以B/C重组株的形式传入中国并在中国各地传播的。2020年12月31日前保存的HIV-1 C亚型和其他一些亚型的包膜序列从洛斯阿拉莫斯HIV数据库和中国国家艾滋病/性病预防控制中心数据库下载。对可用序列进行质量筛选，并使用贝叶斯分析建立最大分支可信度进化树，以分析和判断HIV-1 C亚型的起源和传播。HIV-1 C亚型于1952年左右起源于中非，1969年左右传播至南部非洲，1973年左右传播到东部非洲。1977年，来自南部非洲的HIV-1亚型C被引入印度。非洲东部的HIV-1亚型C于1987年被引入巴西。1986年至1989年期间，印度HIV-1 C亚型在三次迁徙事件中出口到中国。中国两个主要的重组子（CRF07_BC和CRF08_BC）分别出现在1988年和1990年。其他B/C重组体，即CRF64_BC、CRF61_BC和CRF62_BC，分别起源于1993年、2002年和2000年。我们的研究重建了HIV-1 C亚型的全球起源和进化史。此外，我们的研究表明，中国HIV-1 C亚型起源于20世纪80年代中后期左右的三个相关的印度谱系，从那时起，与B亚型形成了一些B/C重组体，并在中国引起了广泛的流行。

{"title":"Global Transmission of Human Immunodeficiency Virus 1 Subtype C and Its Impact on the Circulation of B/C Recombination Strains in China","authors":"Zhanmou Liu, Yanling Liang, Yi Feng, Kang Li, Y. Shao","doi":"10.1097/IM9.0000000000000102","DOIUrl":"https://doi.org/10.1097/IM9.0000000000000102","url":null,"abstract":"Abstract This study aimed to reconstruct the origin and worldwide epidemic history of human immunodeficiency virus (HIV) 1 subtype C and comprehend how HIV-1 subtype C was introduced into and spread throughout China in the form of B/C recombinant strains. Envelope sequences of HIV-1 subtype C and some other subtypes deposited before December 31, 2020 were downloaded from the Los Alamos HIV Database and the Chinese National Center for AIDS/STD Control and Prevention Database. The available sequences were screened for quality, and Bayesian analysis was used to build the maximum clade credibility evolutionary tree to analyze and judge the origin and spread of HIV-1 subtype C. HIV-1 subtype C originated in central Africa around 1952, then spread to southern Africa around 1969 and to eastern Africa around 1973. HIV-1 subtype C from southern Africa was introduced into India in 1977. HIV-1 subtype C of eastern Africa was introduced into Brazil in 1987. Indian HIV-1 subtype C was exported to China in three migration events during the period from 1986 to 1989. The two predominant recombinants in China (CRF07_BC and CRF08_BC) emerged in 1988 and 1990, respectively. Other B/C recombinants, namely, CRF64_BC, CRF61_BC and CRF62_BC, originated in 1993, 2002 and 2000, respectively. Our study has reconstructed the global origin and evolutionary history of HIV-1 subtype C. In addition, our study demonstrated that the Chinese HIV-1 subtype C originated from three related Indian lineages around the mid to late 1980s and, since then, has formed some B/C recombinants with subtype B that caused a widespread epidemic in China.","PeriodicalId":73374,"journal":{"name":"Infectious microbes & diseases","volume":"4 1","pages":"157 - 160"},"PeriodicalIF":0.0,"publicationDate":"2022-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42217393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The group A Streptococcus interleukin-8 protease SpyCEP promotes bacterial intracellular survival by evasion of autophagy. A群链球菌白细胞介素-8蛋白酶SpyCEP通过逃避自噬促进细菌胞内存活。

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-09-01 DOI: 10.1097/im9.0000000000000098

René Bergmann, Giuseppe Gulotta, Federica Andreoni, Tomoko Sumitomo, Shigetada Kawabata, Annelies S Zinkernagel, Gursharan S Chhatwal, Victor Nizet, Manfred Rohde, Satoshi Uchiyama

Autophagy serves an innate immune function in defending the host against invading bacteria, including group A Streptococcus (GAS). Autophagy is regulated by numerous host proteins, including the endogenous negative regulator calpain, a cytosolic protease. Globally disseminated serotype M1T1 GAS strains associated with high invasive disease potential express numerous virulence factors and resist autophagic clearance. Upon in vitro infection of human epithelial cell lines with representative wild-type GAS M1T1 strain 5448 (M1.5448), we observed increased calpain activation linked to a specific GAS virulence factor, the IL-8 protease SpyCEP. Calpain activation inhibited autophagy and decreased capture of cytosolic GAS in autophagosomes. In contrast, the serotype M6 GAS strain JRS4 (M6.JRS4), which is highly susceptible to host autophagy-mediated killing, expresses low levels of SpyCEP and does not activate calpain. Overexpression of SpyCEP in M6.JRS4 stimulated calpain activation, inhibited autophagy and significantly decreased bacterial capture in autophagosomes. These paired loss- and gain-of-function studies reveal a novel role for the bacterial protease SpyCEP in enabling GAS M1 evasion of autophagy and host innate immune clearance.

自噬在保护宿主免受入侵细菌(包括A群链球菌(GAS))的侵害方面具有先天免疫功能。自噬受多种宿主蛋白调控，包括内源性负调节因子钙蛋白酶(一种胞质蛋白酶)。全球传播的血清型M1T1 GAS菌株与高侵袭性疾病相关，表达多种毒力因子并抵抗自噬清除。在体外感染具有代表性的野生型GAS M1T1菌株5448 (M1.5448)的人上皮细胞系后，我们观察到与特定GAS毒力因子IL-8蛋白酶SpyCEP相关的calpain激活增加。激活钙蛋白酶抑制自噬，减少自噬小体中胞质GAS的捕获。相比之下，血清型M6 GAS菌株JRS4 (M6.JRS4)对宿主自噬介导的杀伤高度敏感，表达低水平的SpyCEP，不激活calpain。SpyCEP在M6中的过表达。JRS4刺激calpain活化，抑制自噬，显著降低自噬体中的细菌捕获。这些配对的功能丧失和功能获得的研究揭示了细菌蛋白酶SpyCEP在使GAS M1逃避自噬和宿主先天免疫清除中的新作用。

{"title":"The group A Streptococcus interleukin-8 protease SpyCEP promotes bacterial intracellular survival by evasion of autophagy.","authors":"René Bergmann, Giuseppe Gulotta, Federica Andreoni, Tomoko Sumitomo, Shigetada Kawabata, Annelies S Zinkernagel, Gursharan S Chhatwal, Victor Nizet, Manfred Rohde, Satoshi Uchiyama","doi":"10.1097/im9.0000000000000098","DOIUrl":"https://doi.org/10.1097/im9.0000000000000098","url":null,"abstract":"Autophagy serves an innate immune function in defending the host against invading bacteria, including group A Streptococcus (GAS). Autophagy is regulated by numerous host proteins, including the endogenous negative regulator calpain, a cytosolic protease. Globally disseminated serotype M1T1 GAS strains associated with high invasive disease potential express numerous virulence factors and resist autophagic clearance. Upon in vitro infection of human epithelial cell lines with representative wild-type GAS M1T1 strain 5448 (M1.5448), we observed increased calpain activation linked to a specific GAS virulence factor, the IL-8 protease SpyCEP. Calpain activation inhibited autophagy and decreased capture of cytosolic GAS in autophagosomes. In contrast, the serotype M6 GAS strain JRS4 (M6.JRS4), which is highly susceptible to host autophagy-mediated killing, expresses low levels of SpyCEP and does not activate calpain. Overexpression of SpyCEP in M6.JRS4 stimulated calpain activation, inhibited autophagy and significantly decreased bacterial capture in autophagosomes. These paired loss- and gain-of-function studies reveal a novel role for the bacterial protease SpyCEP in enabling GAS M1 evasion of autophagy and host innate immune clearance.","PeriodicalId":73374,"journal":{"name":"Infectious microbes & diseases","volume":"4 3","pages":"116-123"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10275413/pdf/nihms-1867112.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10084943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Bicarbonate Effects on Antibacterial Immunity and Mucus Glycobiology in the Cystic Fibrosis Lung: A Review With Selected Experimental Observations. 碳酸氢盐对囊性纤维化肺的抗菌免疫和粘液糖生物学的影响:部分实验观察的综述。

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-09-01 DOI: 10.1097/im9.0000000000000101

Ruth Siew, Tzung-Lin Ou, Samira Dahesh, Kathryn Akong, Victor Nizet

The primary defect in cystic fibrosis (CF) is abnormal chloride and bicarbonate transport in the cystic fibrosis transmembrane conductance regulator (CFTR) epithelial ion channel. The apical surface of the respiratory tract is lined by an airway surface liquid layer (ASL) composed of mucin comprising mainly MUC5A and MUC5B glycoproteins. ASL homeostasis depends on sodium bicarbonate secretion into the airways and secretion deficits alter mucus properties leading to airway obstruction, inflammation, and infections. Downstream effects of abnormal ion transport in the lungs include altered intrinsic immune defenses. We observed that neutrophils killed Pseudomonas aeruginosa more efficiently when it had been exposed to sodium bicarbonate, and formation of neutrophil extracellular traps (NETs) by neutrophils was augmented in the presence of increasing bicarbonate concentrations. Physiological levels of bicarbonate sensitized P. aeruginosa to the antimicrobial peptide cathelicidin LL-37, which is present in both lung ASL and in NETs. Sodium bicarbonate has various uses in clinical medicine and in the care of CF patients, and could be further explored as a therapeutic adjunct against Pseudomonas infections.

囊性纤维化(CF)的主要缺陷是囊性纤维化跨膜传导调节剂(CFTR)上皮离子通道中氯离子和碳酸氢盐转运异常。呼吸道的顶端表面有一层由粘蛋白组成的气道表面液层(ASL)，主要由MUC5A和MUC5B糖蛋白组成。ASL的内稳态依赖于碳酸氢钠分泌到气道，分泌不足会改变粘液特性，导致气道阻塞、炎症和感染。肺中异常离子运输的下游效应包括改变内在免疫防御。我们观察到中性粒细胞在暴露于碳酸氢钠时更有效地杀死铜绿假单胞菌，并且在碳酸氢钠浓度增加的情况下，中性粒细胞形成的中性粒细胞胞外陷阱(NETs)增加。生理水平的碳酸氢盐使P. aeruginosa对抗菌肽cathelicidin LL-37敏感，该肽存在于肺ASL和NETs中。碳酸氢钠在临床医学和CF患者的护理中有多种用途，可以进一步探索作为假单胞菌感染的治疗辅助药物。

{"title":"Bicarbonate Effects on Antibacterial Immunity and Mucus Glycobiology in the Cystic Fibrosis Lung: A Review With Selected Experimental Observations.","authors":"Ruth Siew, Tzung-Lin Ou, Samira Dahesh, Kathryn Akong, Victor Nizet","doi":"10.1097/im9.0000000000000101","DOIUrl":"https://doi.org/10.1097/im9.0000000000000101","url":null,"abstract":"The primary defect in cystic fibrosis (CF) is abnormal chloride and bicarbonate transport in the cystic fibrosis transmembrane conductance regulator (CFTR) epithelial ion channel. The apical surface of the respiratory tract is lined by an airway surface liquid layer (ASL) composed of mucin comprising mainly MUC5A and MUC5B glycoproteins. ASL homeostasis depends on sodium bicarbonate secretion into the airways and secretion deficits alter mucus properties leading to airway obstruction, inflammation, and infections. Downstream effects of abnormal ion transport in the lungs include altered intrinsic immune defenses. We observed that neutrophils killed Pseudomonas aeruginosa more efficiently when it had been exposed to sodium bicarbonate, and formation of neutrophil extracellular traps (NETs) by neutrophils was augmented in the presence of increasing bicarbonate concentrations. Physiological levels of bicarbonate sensitized P. aeruginosa to the antimicrobial peptide cathelicidin LL-37, which is present in both lung ASL and in NETs. Sodium bicarbonate has various uses in clinical medicine and in the care of CF patients, and could be further explored as a therapeutic adjunct against Pseudomonas infections.","PeriodicalId":73374,"journal":{"name":"Infectious microbes & diseases","volume":"4 3","pages":"103-110"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9928163/pdf/nihms-1827705.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9639310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Introducing the New Versions of Chinese Diagnosis and Treatment Protocol for COVID-19 新冠肺炎中国诊疗方案新版本介绍

Q3 INFECTIOUS DISEASES

Infectious microbes & diseases

Pub Date : 2022-08-04 DOI: 10.1097/im9.0000000000000099

Qiong Zhang

Since the first outbreak of COVID-19 in January 2020, the pandemic has lasted already for 21⁄2 years, causing 564,126,546 confirmed infections and 6,371,354 confirmed deaths worldwide by July 22, 2022. In addition to the large number of deaths caused by the disease, the COVID-19 pandemic has also had a huge impact on the world economy. Not only have the transportation, tourism, catering, cultural and entertainment industries, and other personnel-intensive industries been directly impacted, but also a large number of people have been isolated and controlled or accepted home office work, which in turn affected all walks of life. According to the World Economic Outlook Report released by the International Monetary Fund in October 2021, the world economy has declined by 3.1% year-on-year in 2020, of which developed economies has declined by 4.5% and emerging market and developing economies by 2.1%. In the process of containing the COVID-19 epidemic, different countries have adopted different antiepidemic strategies, and the results achieved have been variable. China's antiepidemic containment strategies have proven highly effective. Wuhan, as the city where the outbreak was first reported, faced the rapid dissemination of an unknown pathogen. After the initial chaos, the situation was quickly stabilized with the support of personnel and materials from all over the country. Under the organization of the Chinese National Health Commission, the experience and lessons of epidemic prevention and control and clinical treatment have continuously been summarized and updated in national guidelines. Between January 16 and March 3, 2020, eight versions (the Trial Versions 1 to 7 and the Revised Trial Version 5) of theDiagnosis and Treatment Protocol for COVID-19 have been released and updatedwithin a short period

自2020年1月首次爆发COVID-19以来，这场大流行已经持续了21年半，截至2022年7月22日，全球已造成564,126,546例确诊感染和6371,354例确诊死亡。新冠肺炎大流行除了造成大量死亡外，还对世界经济产生了巨大影响。不仅交通、旅游、餐饮、文化娱乐等人员密集型产业受到直接冲击，而且大量人员被隔离控制或接受居家办公，进而影响各行各业。根据国际货币基金组织2021年10月发布的《世界经济展望报告》，2020年世界经济同比下降3.1%，其中发达经济体下降4.5%，新兴市场和发展中经济体下降2.1%。在疫情防控过程中，各国采取了不同的防控策略，取得的效果参差不齐。事实证明，中国的疫情防控战略非常有效。作为首次报告疫情的城市，武汉面临着一种未知病原体的迅速传播。在最初的混乱之后，在来自全国各地的人员和物资的支持下，局势迅速稳定下来。在中国国家卫生健康委员会的组织下，国家指南不断总结和更新疫情防控和临床治疗的经验教训。2020年1月16日至3月3日期间，发布了八个版本的《新冠肺炎诊疗方案》(试验版本1至7和修订的试验版本5)，并在短时间内进行了更新

{"title":"Introducing the New Versions of Chinese Diagnosis and Treatment Protocol for COVID-19","authors":"Qiong Zhang","doi":"10.1097/im9.0000000000000099","DOIUrl":"https://doi.org/10.1097/im9.0000000000000099","url":null,"abstract":"Since the first outbreak of COVID-19 in January 2020, the pandemic has lasted already for 21⁄2 years, causing 564,126,546 confirmed infections and 6,371,354 confirmed deaths worldwide by July 22, 2022. In addition to the large number of deaths caused by the disease, the COVID-19 pandemic has also had a huge impact on the world economy. Not only have the transportation, tourism, catering, cultural and entertainment industries, and other personnel-intensive industries been directly impacted, but also a large number of people have been isolated and controlled or accepted home office work, which in turn affected all walks of life. According to the World Economic Outlook Report released by the International Monetary Fund in October 2021, the world economy has declined by 3.1% year-on-year in 2020, of which developed economies has declined by 4.5% and emerging market and developing economies by 2.1%. In the process of containing the COVID-19 epidemic, different countries have adopted different antiepidemic strategies, and the results achieved have been variable. China's antiepidemic containment strategies have proven highly effective. Wuhan, as the city where the outbreak was first reported, faced the rapid dissemination of an unknown pathogen. After the initial chaos, the situation was quickly stabilized with the support of personnel and materials from all over the country. Under the organization of the Chinese National Health Commission, the experience and lessons of epidemic prevention and control and clinical treatment have continuously been summarized and updated in national guidelines. Between January 16 and March 3, 2020, eight versions (the Trial Versions 1 to 7 and the Revised Trial Version 5) of theDiagnosis and Treatment Protocol for COVID-19 have been released and updatedwithin a short period","PeriodicalId":73374,"journal":{"name":"Infectious microbes & diseases","volume":"4 1","pages":"83 - 84"},"PeriodicalIF":0.0,"publicationDate":"2022-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43347147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9